Abstract
Symbiodinium are symbiotic dinoflagellates that commonly reside in cnidarians e.g. corals and jellyfish. A sustained loss of symbiosis between Symbiodinium and corals results in coral bleaching and eventual death. To help guide risk management of reef systems in light of climate change, the Sea-quence project of the Reef Future Genomics (ReFuGe) 2020 Consortium aims to generate reference genetic data for reef systems at the Great Barrier Reef and the Red Sea. Here we report de novo genome assemblies (coverage >30-fold) from two Symbiodinium isolates of Clades C (origin: Magnetic Island, Australia) and F (Australian National Algae Culture Collection CS-156), and assess the extent of divergence of these genomes relative to other clades and to other eukaryotes. Genome size is computationally estimated at 1.5Gbp (Clade C) and 1.1 Gbp (Clade F), with overall G+C content ~44%. Major phylogenetic markers of nuclear (nr28S, elf2) and organellar genes (cob, coI, psbA, cp23S) were recovered. Of the 458 conserved eukaryote proteins across six model organisms (in CEGMA), we recovered 176 (38%) in Clade C, 149 (33%) in F; the corresponding numbers are higher at 295 (64%) and 267 (58%) when proteins of the chlorophyte Chlamydomonas reinhardtii and apicomplexan Toxoplasma gondii were included in the analysis. This observation suggests high divergence between genomes of Symbiodinium and other eukaryotes. Genome mapping using published transcriptomes (of clades A through D) shows substantial divergence among different clades, with mapped coding regions having higher G+C content (~50%). Our findings support the established inter-clade phylogenetic relationships of Symbiodinium, and suggest a trend of genome reduction from the basal lineage (Clade A; estimated size ~3Gbp) through to the more recently diverged lineages of Clades C and F. These genome data provide an excellent analysis platform for testing numerous biological hypotheses related to algal evolution and adaptation.